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[Ensemble] ENSG biomart
jjbang
2017. 9. 26. 13:43
library(biomaRt)
ensembl=useMart("ensembl") # using ensembl database data
ensembl=useDataset("hsapiens_gene_ensembl",mart=ensembl) # from ensembl using homosapien gene data
dat = as.matrix(read.table('/Volumes/Data1/data/TCGA-bresat/SAAV/4_20170808_breast105_PAV_ano.txt',sep='\t',header=TRUE))
for(i in 1:nrow(dat))
{
key = strsplit(dat[i,12],'/')
for(j in length(key))
{
id=getBM(attributes=c("hgnc_symbol") ,filters = "ensembl_gene_id",values= key[[1]][j], mart= ensembl)
}
}